Contacts of the helix formed by residues 253 - 267 (chain B) in PDB entry 2NYM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B PHE* 3.1 15.9 - + - -
211B ILE* 3.2 28.0 - - + -
212B ALA* 3.7 16.6 - - + +
215B LEU* 3.6 13.5 - - + -
244B LEU* 2.6 49.4 + - + -
247B VAL* 3.0 25.6 - - - +
249B SER* 3.9 10.1 - - - -
250B LEU* 3.5 34.2 - - + +
252B VAL* 1.3 78.4 - - + +
254B HIS* 1.3 59.1 + - - +
255B PRO* 3.5 2.5 - - - -
256B GLN* 3.4 9.5 + - + +
257B LEU* 2.8 32.9 + - + +
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Residues in contact with HIS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B HIS* 4.9 3.0 - + - -
250B LEU* 3.1 34.5 + - + +
253B TYR* 1.3 76.6 - - - +
255B PRO* 1.3 72.2 - - + +
257B LEU* 2.8 9.6 + - - +
258B ALA* 2.8 31.4 + - + +
293B MSE 3.3 60.6 + - + +
294B PHE* 4.7 2.2 - + - -
296B ASN* 4.8 9.4 + - - -
297B GLU* 2.8 45.7 + - + +
300B GLU* 5.2 1.0 + - - -
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Residues in contact with PRO 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B SER 4.7 4.5 - - - +
252B VAL 4.4 5.2 - - - +
253B TYR 3.6 1.1 - - - -
254B HIS* 1.3 101.2 - - + +
256B GLN* 1.3 90.0 + - - +
257B LEU 3.2 0.3 + - - -
258B ALA* 3.9 6.6 - - + +
259B TYR* 3.3 22.0 + - - +
293B MSE 5.3 1.6 - - + -
300B GLU* 5.8 1.3 - - - +
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Residues in contact with GLN 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ALA* 4.0 22.2 - - + +
215B LEU* 4.0 19.8 - - + +
216B GLU* 4.3 25.5 - - + +
252B VAL 3.6 12.9 + - - -
253B TYR* 3.8 17.5 - - - +
255B PRO* 1.3 99.6 - - - +
257B LEU* 1.3 63.0 + - - +
259B TYR* 3.5 14.5 - - - +
260B CYS* 3.6 13.0 + - - -
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LEU* 3.6 15.2 - - + +
241B LEU* 3.4 40.4 - - + +
244B LEU* 4.2 13.0 - - + -
245B HIS* 3.3 43.5 - - + +
250B LEU* 4.0 20.4 - - + -
253B TYR* 2.8 16.3 + - + +
254B HIS* 2.8 10.8 + - - +
256B GLN* 1.3 72.8 - - - +
258B ALA* 1.3 57.1 + - - +
259B TYR 3.0 1.3 - - - -
260B CYS* 2.4 39.2 + - - +
261B VAL* 3.2 6.8 + - + -
297B GLU* 4.7 0.9 - - - +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B HIS* 2.8 20.2 + - + +
255B PRO* 3.9 7.4 - - + +
257B LEU* 1.3 71.2 - - - +
259B TYR* 1.3 52.5 + - - +
261B VAL* 2.9 6.2 + - - +
262B VAL* 2.7 38.8 + - + +
297B GLU* 3.6 38.3 + - + +
300B GLU* 3.9 22.7 - - - +
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLY* 4.4 25.4 - - - -
220B SER 5.2 0.4 - - - -
223B ASN* 4.1 11.1 + - + +
255B PRO 3.3 10.8 + - - +
256B GLN* 3.5 14.4 - - - +
257B LEU 2.7 4.2 + - - -
258B ALA* 1.3 74.8 - - - +
260B CYS* 1.3 57.2 + - - +
262B VAL* 3.7 5.8 - - + +
263B GLN* 2.7 77.3 + - + +
300B GLU* 5.2 2.6 + - - -
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Residues in contact with CYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LEU* 3.5 38.6 - - - -
218B LEU* 4.3 3.4 - - - -
219B GLY* 4.1 9.2 - - - -
222B ILE* 3.6 29.0 - - + +
241B LEU* 3.7 20.4 - - + -
256B GLN 3.7 11.2 - - - -
257B LEU 2.4 24.2 + - - +
259B TYR* 1.3 74.3 - - - +
261B VAL* 1.3 55.0 + - - +
263B GLN* 4.4 0.4 - - - -
264B PHE* 2.9 31.9 + - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LEU* 4.7 5.8 - - + -
241B LEU* 5.1 4.7 - - + -
242B LEU* 4.5 6.7 - - + -
245B HIS* 4.1 17.3 - - + -
257B LEU* 3.8 14.4 - - + +
258B ALA* 2.9 10.9 + - - +
260B CYS* 1.3 75.9 - - - +
262B VAL* 1.3 65.1 + - + +
264B PHE* 3.1 8.9 + - - +
265B LEU* 3.0 22.2 + - + +
275B VAL* 3.5 38.4 - - + -
297B GLU* 3.6 24.9 - - - +
301B ILE* 4.4 9.2 - - + -
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Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ALA* 2.7 22.9 + - + +
259B TYR* 3.7 5.2 - - - +
261B VAL* 1.3 73.0 - - - +
263B GLN* 1.3 66.8 + - - +
265B LEU* 2.6 32.8 + - - +
266B GLU* 3.1 24.3 + - + +
297B GLU* 5.2 0.9 - - + +
300B GLU* 3.6 46.9 - - + +
301B ILE* 4.4 10.8 - - + -
304B VAL* 4.7 10.3 - - + +
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Residues in contact with GLN 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLY 5.4 0.2 - - - +
222B ILE* 4.2 11.8 - - + +
223B ASN* 3.6 35.6 + - + +
259B TYR* 2.7 65.1 + - + +
260B CYS* 4.0 3.8 - - - +
262B VAL* 1.3 81.9 - - - +
264B PHE* 1.3 60.1 + - - +
266B GLU* 3.5 35.1 + - - +
267B LYS* 3.5 13.3 + - - +
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Residues in contact with PHE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ILE* 3.2 45.3 - - + -
225B PHE* 3.6 23.3 - + - -
229B LEU* 4.4 10.9 - - + +
233B HIS* 3.5 27.1 - - + -
236B PHE* 3.9 13.7 - + - -
237B LEU* 3.2 48.2 - - + -
241B LEU* 4.5 0.4 - - + -
260B CYS 2.9 15.5 + - - +
261B VAL 3.2 5.6 - - - +
262B VAL 3.0 0.2 - - - -
263B GLN* 1.3 79.6 - - - +
265B LEU* 1.3 61.3 + - + +
267B LYS* 3.4 13.0 + - + +
268B ASP* 3.7 11.6 + - - +
271B LEU* 3.8 15.8 - - + +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B VAL 3.0 14.4 + - - +
262B VAL* 2.6 17.7 + - - +
264B PHE* 1.3 72.1 - - + +
266B GLU* 1.3 60.3 + - - -
267B LYS 3.3 0.2 - - - -
268B ASP 3.9 5.6 - - - +
269B SER* 3.3 26.4 + - - -
271B LEU* 3.5 15.9 - - + +
272B THR* 3.2 51.8 - - + +
275B VAL* 4.5 19.7 - - + -
301B ILE* 3.6 35.2 - - + +
304B VAL* 5.2 11.4 - - + +
305B ILE* 6.3 0.9 - - - -
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Residues in contact with GLU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B VAL* 3.1 19.2 + - + +
263B GLN* 3.8 29.6 + - - +
264B PHE 3.2 0.6 - - - -
265B LEU* 1.3 76.7 - - - +
267B LYS* 1.3 58.3 + - - +
268B ASP 3.2 3.2 + - - -
269B SER 5.2 0.4 + - - -
304B VAL* 4.0 33.0 - - + +
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ILE* 5.0 14.6 - - + +
223B ASN* 6.1 1.3 - - - -
224B GLY 6.1 0.4 - - - +
225B PHE* 5.6 4.0 - - + +
227B LEU 4.6 8.8 - - - +
229B LEU* 4.0 19.3 - - + +
263B GLN 3.5 9.3 + - - +
264B PHE* 3.4 11.7 + - + +
265B LEU 3.3 0.6 - - - -
266B GLU* 1.3 79.8 - - - +
268B ASP* 1.3 63.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il